The Australian has been on loan at The Den since November and has made a good impression on manager Kenny Jackett during his nine appearances.
Lowry, 22, has signed a two-and-a-half-year deal for the Lions and is looking forward to returning from suspension and rewarding his manager's faith.
"It was [an easy decision to make]," Lowry told the club's official website. "Since my first home game against Doncaster the fans have taken really well to me.
"It came about quite quickly, I had a good chat with the gaffer and he made it clear he wanted to sign me. I'm really happy to commit myself to this football club.
"I'm an ambitious person and I want to play in the Premier League so why can't we get there with Millwall?"